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Summary A dynamic assembly of nuclear and cytoplasmic processes regulate gene activity. Hypoxic stress and the associated energy crisis activate a plurality of regulatory mechanisms including modulation of chromatin structure, transcriptional activation and post‐transcriptional processes. Temporal control of genes is associated with specific chromatin modifications and transcription factors. Genome‐scale technologies that resolve transcript subpopulations in the nucleus and cytoplasm indicate post‐transcriptional processes enable cells to conserve energy, prepare for prolonged stress and accelerate recovery. Moreover, the harboring of gene transcripts associated with growth in the nucleus and macromolecular RNA–protein complexes contributes to the preferential translation of stress‐responsive gene transcripts during hypoxia. We discuss evidence of evolutionary variation in integration of nuclear and cytoplasmic processes that may contribute to variations in flooding resilience.
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This content will become publicly available on October 1, 2025
An RNA-centric view of transcription and genome organization
Foundational models of transcriptional regulation involve the assembly of protein complexes at DNA elements associated with specific genes. These assemblies, which can include transcription factors, cofactors, RNA polymerase, and various chromatin regulators, form dynamic spatial compartments that contribute to both gene regulation and local genome architecture. This DNA-protein-centric view has been modified with recent evidence that RNA molecules have important roles to play in gene regulation and genome structure. Here, we discuss evidence that gene regulation by RNA occurs at multiple levels that include assembly of transcriptional complexes and genome compartments, feedback regulation of active genes, silencing of genes, and control of protein kinases. We thus provide an RNA-centric view of transcriptional regulation that must reside alongside the more traditional DNA-protein-centric perspectives on gene regulation and genome architecture.
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- Award ID(s):
- 2044895
- PAR ID:
- 10572498
- Publisher / Repository:
- CellPress
- Date Published:
- Journal Name:
- Molecular Cell
- Volume:
- 84
- Issue:
- 19
- ISSN:
- 1097-2765
- Page Range / eLocation ID:
- 3627 to 3643
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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